Our group develops, maintains and contributes to many large software projects and libraries for applications in systems biology and bioinformatics.
Most projects are managed on the GitHub page of the group:
With this Java™-based program, popular file formats that are used for graphical representations in systems biology modelling can be converted into one another: Escher's JSON dialect as well as the standardized formats SBML and SBGN-ML. The program can be operated either via its graphical user interface or via the command line.
InCroMAP offers a variety of possibilities to visualize data sets or to apply methods for integrated cross-platform analysis. Currently, numerous data formats such as mRNA, miRNA, DNA methylation and protein modification are supported. InCroMAP can map and analyze all data in the context of biological networks.
InSilico is a project based on Eclipse and JavaFX for the integration and management of various apps to facilitate the processing of scientific models and data as well as the development of end-user software. Here you will find detailed Dokumentation and further project descriptions.
KEGGtranslator offers a visual representation of biological networks from the popular KEGG database as well as a variety of options for converting the files submitted there into standardized formats. The Java™-based program supports current versions of BioPAX, SBML, GraphML, and numerous other formats.
SBML2LaTeX generates human-readable reports in LaTeX format about the content of SBML files. These can then be converted into various formats, such as PDF files. The generated content can also be integrated directly into publications since the equations contained in SBML are also translated into formulas.
SBMLsqueezer analyzes biochemical reactions and automatically suggests a set of applicable kinetic equations. Either the equations can be generated automatically for the entire reaction system at once, or for selected biochemical reactions. The program creates contained kinetic parameters and derives their unit itself. This feature makes it easy to convert structural models to dynamic models and then simulate them.
SBSCL is a comprehensive implementation of systems biology simulation methods in Java™. SBSCL can solve complex differential equation systems (including delays, algebraic systems, spontaneous events, and rules) as well as flow balance analysis using the Simplex method. Currently, an interpreter for SBML models is built in. Extensions for other formats are possible. Due to the integrated support of SED-ML, simulation experiments can be clearly repeated.
TFpredict uses methods of monitored machine learning to differentiate transcription factors or σ factors from other proteins and then characterize them structurally.